Basic Information
Locus ID:
Ag2G02459
Species & Taxonomic ID:
Apium graveolens & 4045
Genome Assembly:
GCA_009905375.1
Description:
RING-type E3 ubiquitin transferase
Maps and Mapping Data
| Chromosome | Start | End | Strand | ID |
|---|---|---|---|---|
| chr2 | 287851109 | 287859487 | + | Ag2G02459 |
Protein Data
Protein Properties:
| Theoretical pI | Molecular Weight | Instability Index | Aliphatic Index | GRAVY |
|---|---|---|---|---|
| 5.34 | 122,672.32 Da | 39.45 | 93.79 | -0.19 |
Protein Domain:
| Category | ID | Description | Start | End | Evalue/Score | InterPro ID |
|---|---|---|---|---|---|---|
| CDD | cd00164 | S1_like | 182 | 242 | 6.33094E-4 | - |
| Pfam | PF00400 | WD domain, G-beta repeat | 865 | 897 | 0.021 | IPR001680 |
| Pfam | PF00575 | S1 RNA binding domain | 64 | 129 | 2.5E-13 | IPR003029 |
| SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 167 | 242 | 1.19E-5 | IPR012340 |
| SUPERFAMILY | SSF48371 | ARM repeat | 375 | 806 | 1.2E-7 | IPR016024 |
| SUPERFAMILY | SSF50978 | WD40 repeat-like | 828 | 1108 | 2.75E-34 | IPR036322 |
| SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 59 | 133 | 1.49E-18 | IPR012340 |
| Gene3D | G3DSA:2.130.10.10 | - | 926 | 1109 | 7.8E-15 | IPR015943 |
| Gene3D | G3DSA:1.25.10.10 | - | 391 | 670 | 6.9E-7 | IPR011989 |
| Gene3D | G3DSA:2.40.50.140 | - | 172 | 262 | 1.1E-6 | - |
| Gene3D | G3DSA:2.40.50.140 | - | 56 | 136 | 1.5E-19 | - |
| Gene3D | G3DSA:2.130.10.10 | - | 789 | 925 | 1.2E-13 | IPR015943 |
| SMART | SM00320 | WD40_4 | 989 | 1025 | 160.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 1028 | 1064 | 92.0 | IPR001680 |
| SMART | SM00320 | WD40_4 | 933 | 976 | 76.0 | IPR001680 |
| SMART | SM00316 | S1_6 | 175 | 251 | 0.04 | IPR022967 |
| SMART | SM00316 | S1_6 | 62 | 133 | 2.0E-19 | IPR022967 |
| SMART | SM00320 | WD40_4 | 1067 | 1107 | 0.28 | IPR001680 |
| SMART | SM00320 | WD40_4 | 859 | 898 | 2.8E-5 | IPR001680 |
| SMART | SM00320 | WD40_4 | 817 | 854 | 6.0 | IPR001680 |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 1075 | 1109 | 10.274523 | IPR001680 |
| ProSiteProfiles | PS50126 | S1 domain profile. | 177 | 251 | 12.664097 | IPR003029 |
| ProSiteProfiles | PS50126 | S1 domain profile. | 64 | 133 | 20.291121 | IPR003029 |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 866 | 901 | 9.361965 | - |
| ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 1075 | 1109 | 9.968326 | - |
| ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 866 | 901 | 11.176815 | IPR001680 |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 139 | 172 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 34 | 57 | - | - |
| MobiDBLite | mobidb-lite | consensus disorder prediction | 131 | 172 | - | - |
Gene Ontology
Molecular Function:
Best hit
| Source | Best Hit ID | Description | E-value |
|---|---|---|---|
| TAIR | AT4G29060.2 | elongation factor Ts family protein. | 0 |
| RefSeq | XP_017237523.1 | PREDICTED: putative E3 ubiquitin-protein ligase LIN-1 [Daucus carota subsp. sativus] | 0 |
| C6L7U1 | Putative E3 ubiquitin-protein ligase LIN-1 OS=Lotus japonicus OX=34305 GN=CERBERUS PE=2 SV=2 | 0 | |
| TrEMBL | A0A166ASA6 | RING-type E3 ubiquitin transferase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_010478 PE=4 SV=1 | 0 |
Expression
| BioProject | Accession | TPM | Cultivar | Tissue | Development Stage | Sample Name | Description |
|---|---|---|---|---|---|---|---|
| PRJNA723697 | SRX10692252 | 0.082636 | Shengqin NO.2 | seed | S1-1 | S1-1 | initial formation stage (S1) |
| PRJNA723697 | SRX10692254 | 0.049192 | Shengqin NO.2 | seed | S1-3 | S1-3 | initial formation stage (S1) |
| PRJNA723697 | SRX10692255 | 0.060467 | Shengqin NO.2 | seed | S3-1 | S3-1 | middle development stage (S3) |
| PRJNA723697 | SRX10692256 | 0 | Shengqin NO.2 | seed | S3-2 | S3-2 | middle development stage (S3) |
| PRJNA723697 | SRX10692257 | 0 | Shengqin NO.2 | seed | S3-3 | S3-3 | middle development stage (S3) |
| PRJNA723697 | SRX10692258 | 0.188934 | Shengqin NO.2 | seed | S5-1 | S5-1 | maturation stage (S5) |
| PRJNA723697 | SRX10692259 | 0.103724 | Shengqin NO.2 | seed | S5-2 | S5-2 | maturation stage (S5) |
| PRJNA723697 | SRX10692260 | 0.079969 | Shengqin NO.2 | seed | S5-3 | S5-3 | maturation stage (S5) |
| PRJNA884666 | SRX17729272 | 0.036076 | celery | anther | W99A-r1 | male sterile line | |
| PRJNA884666 | SRX17729273 | 0.039838 | celery | anther | W99A-r2 | male sterile line | |
| PRJNA884666 | SRX17729274 | 0.111179 | celery | anther | W99A-r3 | male sterile line | |
| PRJNA884666 | SRX17729275 | 0.274639 | celery | anther | W99B-r1 | maintainer line | |
| PRJNA884666 | SRX17729276 | 0.09733 | celery | anther | W99B-r2 | maintainer line | |
| PRJNA884666 | SRX17729277 | 0.161198 | celery | anther | W99B-r3 | maintainer line | |
| PRJNA884180 | SRX17743889 | 0.122292 | var. secalinum Yablochny | collenchyma | Col_S1_rep1-1 | ||
| PRJNA884180 | SRX17748056 | 0.419561 | var. secalinum Yablochny | collenchyma | Col_S1_rep3 | biological replicate 3 | |
| PRJNA884180 | SRX17748057 | 0.089997 | var. secalinum Yablochny | collenchyma | Col_S1_rep4 | biological replicate 4 | |
| PRJNA884180 | SRX17748678 | 0.184366 | var. secalinum Yablochny | parenchyma | Par_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748679 | 0.083549 | var. secalinum Yablochny | parenchyma | Par_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748680 | 0.324359 | var. secalinum Yablochny | parenchyma | Par_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748681 | 0.249414 | var. secalinum Yablochny | parenchyma | Par_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17748898 | 0 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17748899 | 0.152738 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17748900 | 0.094164 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17748901 | 0.159807 | var. secalinum Yablochny | vascular bundle | Vas_S1_rep4 | Biological replicate 4 | |
| PRJNA884180 | SRX17749129 | 0.022096 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep1 | Biological replicate 1 | |
| PRJNA884180 | SRX17749130 | 0 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep2 | Biological replicate 2 | |
| PRJNA884180 | SRX17749131 | 0 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep3 | Biological replicate 3 | |
| PRJNA884180 | SRX17749132 | 0 | var. secalinum Yablochny | part of the celery petiole without collenchyma strands | Collenchyma-free_S1_rep4 | Biological replicate 4 | |
| PRJNA1124269 | SRX24936411 | 0 | leaf | CK1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936412 | 0 | leaf | CK2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936413 | 0 | leaf | CK3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936414 | 0.200344 | leaf | D1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936415 | 0.447969 | leaf | D2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936416 | 0 | leaf | D3 | replicate=biological replicate3 | ||
| PRJNA1124269 | SRX24936417 | 0.041827 | leaf | MD1 | replicate=biological replicate1 | ||
| PRJNA1124269 | SRX24936418 | 0 | leaf | MD2 | replicate=biological replicate2 | ||
| PRJNA1124269 | SRX24936419 | 0.049812 | leaf | MD3 | replicate=biological replicate3 | ||
| PRJNA387092 | SRX2833309 | 0.240031 | shanghaihuangxin | leaf | leaves between 0.5 and 1 cm in breadth, folded; | stage 2 | |
| PRJNA387092 | SRX2833321 | 0.11271 | shanghaihuangxin | leaf | leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion | stage 5 | |
| PRJNA387092 | SRX2833323 | 0.148483 | shanghaihuangxin | leaf | leaves >3 cm, unfolded, with clearstem extension | stage 7 | |
| PRJNA543957 | SRX5879598 | 0.585939 | Zhangzhou lvqing | stem | Se3 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879599 | 0.271692 | Zhangzhou lvqing | stem | Se2 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879600 | 0.026293 | Zhangzhou lvqing | stem | Mock2 | mock | |
| PRJNA543957 | SRX5879601 | 0 | Zhangzhou lvqing | stem | Mock1 | mock | |
| PRJNA543957 | SRX5879602 | 0.378039 | Zhangzhou lvqing | stem | Se1 | 100 ppm Na2SeO4 | |
| PRJNA543957 | SRX5879603 | 0.086164 | Zhangzhou lvqing | stem | Mock3 | mock | |
| PRJNA609149 | SRX7815917 | 0.199803 | Jinnan Shiqin | flower bud | early flower bud | early flower bud | |
| PRJNA609149 | SRX7815918 | 0 | Jinnan Shiqin | flower bud | middle flower bud | middle flower bud | |
| PRJNA609149 | SRX7815919 | 0.03271 | Jinnan Shiqin | flower bud | early flowering period | early flowering period |
Orthology
| Family | Species | Count | Orthologous Genes |
|---|---|---|---|
| Acanthaceae | Avicennia marina | 6 | jg11768, jg11769, jg11770, jg11771, jg31633, jg31634 |
| Anacardiaceae | Pistacia vera | 2 | pistato.v30049320, pistato.v30256780 |
| Apiaceae | Apium graveolens | 3 | Ag2G02459, Ag3G02527, Ag8G00225 |
| Arecaceae | Cocos nucifera | 2 | COCNU_03G011900, COCNU_07G002000 |
| Arecaceae | Phoenix dactylifera | 2 | gene-LOC103702597, gene-LOC103706139 |
| Asparagaceae | Asparagus officinalis | 3 | AsparagusV1_01.1751.V1.1, AsparagusV1_03.2268.V1.1 ... |
| Asteraceae | Flaveria trinervia | 3 | Ftri4G07535, Ftri7G18227, Ftri8G01620 |
| Casuarinaceae | Casuarina equisetifolia | 2 | Ceq03G0877, Ceq06G1516 |
| Casuarinaceae | Casuarina glauca | 2 | Cgl03G0956, Cgl06G1574 |
| Malvaceae | Hibiscus hamabo Siebold & Zucc. | 2 | nbisL1-mrna-141, nbisL1-mrna-8648 |
| Nitrariaceae | Nitraria sibirica | 2 | evm.TU.LG06.710, evm.TU.LG07.1111 |
| Plantaginaceae | Plantago ovata | 2 | Pov_00003863, Pov_00020671 |
| Poaceae | Echinochloa crus-galli | 4 | AH02.91, BH01.509, BH02.80, CH02.102 |
| Poaceae | Eleusine coracana subsp. coracana | 2 | gene-QOZ80_1AG0000840, gene-QOZ80_1BG0049330 |
| Poaceae | Hordeum vulgare | 1 | HORVU.MOREX.r3.3HG0248980.1 |
| Poaceae | Lolium multiflorum | 3 | gene-QYE76_051444, gene-QYE76_051560, gene-QYE76_051566 |
| Poaceae | Oryza coarctata | 2 | Oco01G005770, Oco02G005870 |
| Poaceae | Oryza sativa | 1 | LOC_Os01g12930.1 |
| Poaceae | Paspalum vaginatum | 1 | gene-BS78_03G006500 |
| Poaceae | Puccinellia tenuiflora | 1 | Pt_Chr0204871 |
| Poaceae | Sporobolus alterniflorus | 1 | Chr21G016220 |
| Poaceae | Thinopyrum elongatum | 1 | Tel3E01G274000 |
| Poaceae | Triticum dicoccoides | 2 | gene_TRIDC3AG020830, gene_TRIDC3BG031130 |
| Poaceae | Triticum aestivum | 3 | TraesCS3A02G154900.1, TraesCS3B02G181200.1 ... |
| Poaceae | Zea mays | 1 | Zm00001eb119290_P001 |
| Poaceae | Zoysia japonica | 5 | nbis-gene-24273, nbis-gene-24274, nbis-gene-32721 ... |
| Poaceae | Zoysia macrostachya | 2 | Zma_g7183, Zma_g9505 |
| Rhizophoraceae | Bruguiera sexangula | 3 | evm.TU.Scaffold_10_RagTag.437, evm.TU.Scaffold_4_RagTag.1931 ... |
| Rhizophoraceae | Carallia pectinifolia | 3 | nbisL1-mrna-13099, nbisL1-mrna-16388, nbisL1-mrna-25645 |
| Rhizophoraceae | Ceriops tagal | 2 | nbisL1-mrna-12295, nbisL1-mrna-6585 |
| Rhizophoraceae | Ceriops zippeliana | 4 | nbisL1-mrna-13044, nbisL1-mrna-13045, nbisL1-mrna-16830 ... |
| Rhizophoraceae | Kandelia candel | 4 | add.evm.TU.utg000018l.158, add.evm.TU.utg000033l.95 ... |
| Rhizophoraceae | Kandelia obovata | 3 | Maker00000143, Maker00011993, Maker00014879 |
| Rhizophoraceae | Rhizophora apiculata | 2 | nbisL1-mrna-20232, nbisL1-mrna-23194 |
| Salicaceae | Populus euphratica | 5 | populus_peu15357, populus_peu21947, populus_peu33000 ... |
| Solanaceae | Lycium barbarum | 2 | gene-LOC132603413, gene-LOC132622109 |
| Solanaceae | Solanum pennellii | 3 | gene-LOC107017250, gene-LOC107025502, gene-LOC114077896 |